In this project we will develop new methods to investigate the three dimensional arrangement of the genome in various cell types from mouse bone marrow. The three dimensional organization of the genome, how it is physically arranged in the nucleus of cells, is recognized as an important component of genome control. The mechanisms by which genes get switched on and off in the correct cells or tissue type, and during the correct stages of development include changes in the spatial organization of the genome. We will develop a new method that can assess three dimensional genome organizations in thousands of individual cells and simultaneously measure the actual gene expression profile of a large number of those cells. We will systematically analyze the data mathematically and statistically to look for new principles of genome organization that may play unknown roles in controlling the genome in health and disease. We will also use the data to generate 3D computer models of individual chromosomes and the entire genome as it exists in the individual cell nucleus. We will then use these models to look for spatial patterns, recurring structures and variable structured regions of the genome that may be important in gene control. For these experiments we will use mouse bone marrow cells, which are an important representative of human bone marrow cells. Bone marrow is a clinically important, complex tissue containing the adult stems cells that give rise to all cells of the blood and immune system. By systematically analyzing the 3D genome conformation and gene expression profiles of these important cell types we will be providing fundamental knowledge of how these cell types function to create the blood. We will cooperate with other research groups to ensure that they have access to these powerful technologies and computer analysis packages that will accelerate a fuller understanding of how the genome is controlled. This information is vital to design new effective therapeutic strategies for the treatment of diseases of the blood and other tissues, and to understand the molecular basis of cancers for more effective treatments and prevention.